Keyboard shortcuts

Press ← or → to navigate between chapters

Press S or / to search in the book

Press ? to show this help

Press Esc to hide this help

The voxelBuilder class

The voxelBuilder class is the primary interface for spheronizator.

Methods

voxelBuilder.reloadConfig(configPath=None)

Parse a configuration file at a provided path, then update attributes.

voxelBuilder.parse(pdbfile, mol2file=None)

Parse protein data from a given PDB file and mol2 file. The mol2 file and PDB file must be for the same protein.

By default, the mol2 file is treated as having the same naming convention as the PDB file. As an example, the command

voxelBuilder.parse(protein_data.pdb)

will look for files with the naming scheme

protein_data.pdb

protein_data.mol2

voxelBuilder.buildData()

Initializes voxel arrays, output arrays, and then builds the output array. Does not take any arguments.

voxelBuilder.check_collision()

Returns True if there has been a collision of two or more atoms located at a specific voxel. Datatype for the output array must not be boolean.

voxelBuilder.find_collision()

Returns the indicies of the output array where two or more atoms have been represented by a single voxel. Dataype must not be boolean.

Attributes

.config

Configuration attribute. See configuration.

.boxSize

Configuration attribute. See configuration.

.voxelSpacing

Configuration attribute. See configuration.

.useFloatVoxels

Configuration attribute. See configuration.

.dataType

Configuration attribute. See configuration.

.useWarnings

Configuration attribute. See configuration.

.useSpheres

Configuration attribute. See configuration.

.bondTypeDict

Dictionary defining the mapping between types of bonds and their locations in the output array.

.atomTypeDict

Dictionary defining the mapping between types of atoms and their locations in the output array.

.structure

Biopython structure object of the parsed protein.

.residues

List of Biopython residue objects located in the structure.

.atoms

List of Biopython atom objects located in the structure.

.resnames

List of all residue names located in the structure.

.voxels

Voxel array which is used to check spatial presence of atoms in the structure. This array should not be changed by hand. It is initialized automatically based on the configuration settings when building the output array.

.output

Output numpy array consisting of the final processed data.

.outputBonds

Bond information array, part of the final processed data.